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2024-11-30	Tao Liu (τν)	Merge pull request #678 from kaizhang/master	commit \| commitdiff \| tree
2024-11-14	Tao Liu (τν)	Update INSTALL.md	commit \| commitdiff \| tree
2024-10-30	Tao Liu (τν)	Update hmmratac.md	commit \| commitdiff \| tree
2024-10-23	Tao Liu (τν)	Merge pull request #668 from macs3-project/feat/macs3...	commit \| commitdiff \| tree
2024-10-22	Tao Liu	rewrite all remaining pyx for callvar to py	commit \| commitdiff \| tree
2024-10-22	Tao Liu	rewrite CallPeakUnit.py	commit \| commitdiff \| tree
2024-10-22	Tao Liu (τν)	Delete MACS3/Signal/CallPeakUnit.py	commit \| commitdiff \| tree
2024-10-22	Tao Liu	changelog	commit \| commitdiff \| tree
2024-10-21	Tao Liu	draft callpeakunit.py	commit \| commitdiff \| tree
2024-10-19	Tao Liu	upload a fragment file for testing	commit \| commitdiff \| tree
2024-10-18	Tao Liu	rewrite scoretrack.py	commit \| commitdiff \| tree
2024-10-18	Tao Liu	rewrite scoretrack.py	commit \| commitdiff \| tree
2024-10-15	Tao Liu	more rewriting on pyx -> py	commit \| commitdiff \| tree
2024-10-15	Tao Liu	implement PETrackII for fragment files from scATAC...	commit \| commitdiff \| tree
2024-10-14	Tao Liu	rewrite some pyx files	commit \| commitdiff \| tree
2024-10-11	Tao Liu	update	commit \| commitdiff \| tree
2024-10-10	Tao Liu	rewrite PeakIO.py, PairedEndTrack.py;	commit \| commitdiff \| tree
2024-10-08	Tao Liu (τν)	Merge pull request #664 from macs3-project/feat/macs3...	commit \| commitdiff \| tree
2024-10-08	Tao Liu	update changelog. prepare temp push	commit \| commitdiff \| tree
2024-10-08	Tao Liu	rewrite BedGraphIO.py	commit \| commitdiff \| tree
2024-10-07	Tao Liu	rewrite BAM.py. Support big-endian in BAM.py/callvar now	commit \| commitdiff \| tree
2024-10-07	Tao Liu	describe the filtering criteria in SAM/BAM/BAMPE parser	commit \| commitdiff \| tree
2024-10-07	Tao Liu	rewrite BAM.py. Support big-endian in BAM.py/callvar now	commit \| commitdiff \| tree
2024-10-07	Tao Liu	rewrite Parser.py. Fix issues in big-endian system.	commit \| commitdiff \| tree
2024-10-05	Tao Liu	rewrite pileupv2.py	commit \| commitdiff \| tree
2024-10-04	Tao Liu	fix bug -- pass int instead of float	commit \| commitdiff \| tree
2024-10-04	Tao Liu	rewrite pileup.py	commit \| commitdiff \| tree
2024-10-04	Tao Liu	rewrite region.py	commit \| commitdiff \| tree
2024-10-04	Tao Liu	rewrite pyx in pure python style for compatibility	commit \| commitdiff \| tree
2024-10-04	Tao Liu (τν)	Merge pull request #662 from macs3-project/feat/macs3...	commit \| commitdiff \| tree
2024-10-03	Tao Liu	reformat other file	commit \| commitdiff \| tree
2024-10-02	Tao Liu	review py codes and remove unused codes	commit \| commitdiff \| tree
2024-10-02	Tao Liu	bug: save digested bdg with incorrect bedGraphIO class	commit \| commitdiff \| tree
2024-10-02	Tao Liu	bug while providing multiple frag files	commit \| commitdiff \| tree
2024-10-02	Tao Liu	move meta informatino to pyproject.toml	commit \| commitdiff \| tree
2024-09-07	Tao Liu (τν)	Update meta.yaml	commit \| commitdiff \| tree
2024-09-07	Tao Liu (τν)	Update index.md (remove an extra space...)	commit \| commitdiff \| tree
2024-09-07	Tao Liu (τν)	Merge pull request #657 from macs3-project/doc/macs3...	commit \| commitdiff \| tree
2024-09-06	Tao Liu	update file format doc name	commit \| commitdiff \| tree
2024-09-06	Tao Liu	put two docs under tutorial	commit \| commitdiff \| tree
2024-09-06	Tao Liu	update date in ChangeLog	commit \| commitdiff \| tree
2024-09-06	Tao Liu	update EOSS icon	commit \| commitdiff \| tree
2024-09-06	Tao Liu	update docs	commit \| commitdiff \| tree
2024-09-06	Tao Liu	update gappedPeak output	commit \| commitdiff \| tree
2024-09-06	Tao Liu	update gappedPeak output	commit \| commitdiff \| tree
2024-07-19	Tao Liu	fix description for --trackline	commit \| commitdiff \| tree
2024-07-19	Tao Liu	avoid numpy2.0.0	commit \| commitdiff \| tree
2024-07-19	Tao Liu	fix description on `--trackline` for callpeak command	commit \| commitdiff \| tree
2024-05-16	Tao Liu (τν)	Merge pull request #645 from macs3-project/feat/macs3...	commit \| commitdiff \| tree
2024-05-16	Tao Liu (τν)	Merge branch 'master' into feat/macs3/narrowpeak	commit \| commitdiff \| tree
2024-05-16	Tao Liu	let hmmratac output narrowpeak with summit and score...	commit \| commitdiff \| tree
2024-05-15	Tao Liu	new function to find peak summit and score by giving...	commit \| commitdiff \| tree
2024-05-15	Tao Liu	move IO functions for bedGraph to BedGraphIO class	commit \| commitdiff \| tree
2024-05-14	Tao Liu	skip the test on SignalProcessing	commit \| commitdiff \| tree
2024-05-14	Tao Liu	update hmmratac narrowpeak output since we now allow...	commit \| commitdiff \| tree
2024-05-14	Tao Liu	still skip cutoffs with 0 peak since avepeak need to...	commit \| commitdiff \| tree
2024-05-14	Tao Liu	cutoff-analysis-max for bdgpeakcall;output rows with...	commit \| commitdiff \| tree
2024-05-14	Tao Liu	add two index md files	commit \| commitdiff \| tree
2024-05-14	Tao Liu	handle error correctly #643	commit \| commitdiff \| tree
2024-05-14	Tao Liu	cutoff analysis	commit \| commitdiff \| tree
2024-05-14	Tao Liu	edit adv tutorial. Add empty files for file formats.	commit \| commitdiff \| tree
2024-05-14	Tao Liu	update changelog	commit \| commitdiff \| tree
2024-05-14	Tao Liu	add option --cutoff-analysis-max for hmmratac	commit \| commitdiff \| tree
2024-05-14	Tao Liu	reorg docs	commit \| commitdiff \| tree
2024-05-14	Tao Liu	reorg docs	commit \| commitdiff \| tree
2024-05-14	Tao Liu	update docs	commit \| commitdiff \| tree
2024-05-14	Tao Liu	update docs	commit \| commitdiff \| tree
2024-05-14	Tao Liu	update	commit \| commitdiff \| tree
2024-05-14	Tao Liu	add more format related files	commit \| commitdiff \| tree
2024-05-14	Tao Liu	reorg md files	commit \| commitdiff \| tree
2024-05-14	Tao Liu	update docs	commit \| commitdiff \| tree
2024-05-14	Tao Liu	#637 -O3 replaces -Ofast	commit \| commitdiff \| tree
2024-05-14	Tao Liu	fix a missing url	commit \| commitdiff \| tree
2024-05-14	Tao Liu	cutoff-analysis-steps option for bdgpeakcall and hmmratac	commit \| commitdiff \| tree
2024-05-14	Tao Liu	add cutoff-analysis-steps to hmmratac	commit \| commitdiff \| tree
2024-05-14	Tao Liu	update hmmratac	commit \| commitdiff \| tree
2024-05-14	Tao Liu	update instructions for conda install	commit \| commitdiff \| tree
2024-05-14	Tao Liu	fix some description	commit \| commitdiff \| tree
2024-05-14	Tao Liu	fix the way to call __close_peak() -- there is no smoothlen	commit \| commitdiff \| tree
2024-05-14	Tao Liu	fix the way to call __close_peak() -- there is no smoothlen	commit \| commitdiff \| tree
2024-05-14	Tao Liu	enable test for SignalProcessing	commit \| commitdiff \| tree
2024-05-14	Tao Liu	clarify the descriptions of enforce_peakyness function	commit \| commitdiff \| tree
2024-05-14	Tao Liu	clarify the descriptions of __close_peak and __close_peak2...	commit \| commitdiff \| tree
2024-05-08	Tao Liu	add two index md files	commit \| commitdiff \| tree
2024-05-07	Tao Liu	update hmmratac results	commit \| commitdiff \| tree
2024-05-07	Tao Liu (τν)	Merge pull request #642 from macs3-project/doc/macs3...	commit \| commitdiff \| tree
2024-05-07	Tao Liu	handle error correctly #643	commit \| commitdiff \| tree
2024-05-03	Tao Liu	cutoff analysis	commit \| commitdiff \| tree
2024-05-03	Tao Liu	edit adv tutorial. Add empty files for file formats.	commit \| commitdiff \| tree
2024-04-27	Tao Liu	update changelog	commit \| commitdiff \| tree
2024-04-26	Tao Liu	add option --cutoff-analysis-max for hmmratac	commit \| commitdiff \| tree
2024-04-26	Tao Liu	reorg docs	commit \| commitdiff \| tree
2024-04-26	Tao Liu	update docs	commit \| commitdiff \| tree
2024-04-26	Tao Liu	update docs	commit \| commitdiff \| tree
2024-04-26	Tao Liu	update	commit \| commitdiff \| tree
2024-04-26	Tao Liu	add more format related files	commit \| commitdiff \| tree
2024-04-26	Tao Liu	reorg md files	commit \| commitdiff \| tree
2024-04-26	Tao Liu	update docs	commit \| commitdiff \| tree
2024-04-26	Tao Liu	#637 -O3 replaces -Ofast	commit \| commitdiff \| tree
2024-04-26	Tao Liu	fix a missing url	commit \| commitdiff \| tree
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